Uganda has joined Rwanda and Burundi in attacking a controversial United Nations report due to be published today that details alleged war crimes committed by their armies in the Democratic Republic of the Congo.

The report covers the conflicts in Congo between 1993 and 2003 and chronicles hundreds of atrocities involving outside forces.

But in a letter to the UN, made public yesterday, Uganda's foreign affairs minister, Sam Kutesa, dismissed the report as "a compendium of rumours deeply flawed in methodology, sourcing and standard of proof".

"Uganda rejects that draft report in its entirety and demands that it not be published," he wrote.

Kutesa said the allegations could make Uganda rethink its commitment to international peacekeeping missions, including in Somalia where its troops form the backbone of the African Union force.

The threat echoed an earlier warning from Rwanda – later withdrawn – that it would pull its troops out of peacekeeping missions, including in Darfur where it pays a key role, if the report was published without amendments.

The Rwandan reaction caused the UN to postpone publication to allow the countries accused of crimes to air their responses alongside the final version. Burundi had also demanded that the allegations against its army be withdrawn.

The delay led to fears among human rights activists that the report would be watered down by the UN for political reasons, with the highly sensitive allegations of possible genocide against Rwanda dropped.

But yesterday the UN high commissioner for human rights, Navi Pillay, whose office compiled the report, said the final version would have no significant changes and that "the substance remains the same".

According to the Associated Press, a leaked copy of the final report revealed that the UN rewrote some sensitive sections, but left intact allegations of genocide.

Despite the changes, the Rwandan foreign affairs minister, Louise Mushikiwabo, said the document was "flawed and dangerous from start to finish".

Ugandan troops entered Congo in 1997, backing rebels who had toppled the dictator Mobutu Sese Seko, and stayed in parts of the country until 2003. UN investigators, who carried out their fieldwork in 2008 and 2009 with the aim of highlighting previously undocumented crimes, said in their draft report that Ugandan troops had committed multiple war crimes, highlighting a "reign of terror" in a Congolese town that lasted several weeks.

"They carried out summary executions of civilians, arbitrarily detained large numbers of people and subjected them to torture and various other cruel, inhuman or degrading treatments," the report said.